{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T04:47:40Z","timestamp":1782967660369,"version":"3.54.5"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2016,10,4]],"date-time":"2016-10-04T00:00:00Z","timestamp":1475539200000},"content-version":"vor","delay-in-days":1460,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,1]]},"DOI":"10.1093\/nar\/gks915","type":"journal-article","created":{"date-parts":[[2012,10,7]],"date-time":"2012-10-07T01:31:23Z","timestamp":1349573483000},"page":"D246-D251","source":"Crossref","is-referenced-by-count":465,"title":["LNCipedia: a database for annotated human lncRNA transcript sequences and structures"],"prefix":"10.1093","volume":"41","author":[{"given":"Pieter-Jan","family":"Volders","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenny","family":"Helsens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaowei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bj\u00f6rn","family":"Menten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lennart","family":"Martens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kris","family":"Gevaert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo","family":"Vandesompele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pieter","family":"Mestdagh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,10,5]]},"reference":[{"key":"key\n\t\t\t\t20171013034749_gks915-B1","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nrg2521","article-title":"Long non-coding RNAs: insights into functions","volume":"10","author":"Mercer","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20171013034749_gks915-B2","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1101\/gad.17446611","article-title":"Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses","volume":"25","author":"Cabili","year":"2011","journal-title":"Genes Dev."},{"key":"key\n\t\t\t\t20171013034749_gks915-B3","doi-asserted-by":"crossref","first-page":"P1","DOI":"10.1186\/gb-2003-5-1-p1","article-title":"Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences","volume":"5","author":"Taft","year":"2003","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20171013034749_gks915-B4","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1016\/j.molcel.2011.08.018","article-title":"Molecular mechanisms of long noncoding RNAs","volume":"43","author":"Wang","year":"2011","journal-title":"Mol. Cell"},{"key":"key\n\t\t\t\t20171013034749_gks915-B5","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/nature10887","article-title":"Modular regulatory principles of large non-coding RNAs","volume":"482","author":"Guttman","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20171013034749_gks915-B6","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/349038a0","article-title":"A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome","volume":"349","author":"Brown","year":"1991","journal-title":"Nature"},{"key":"key\n\t\t\t\t20171013034749_gks915-B7","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1038\/nature08975","article-title":"Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis","volume":"464","author":"Gupta","year":"2010","journal-title":"Nature"},{"key":"key\n\t\t\t\t20171013034749_gks915-B8","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1053\/j.gastro.2006.08.026","article-title":"Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA","volume":"132","author":"Panzitt","year":"2007","journal-title":"Gastroenterology"},{"key":"key\n\t\t\t\t20171013034749_gks915-B9","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/1479-7364-5-2-90","article-title":"Naming \u2018junk\u2019: human non-protein coding RNA (ncRNA) gene nomenclature","volume":"5","author":"Wright","year":"2011","journal-title":"Hum. Genomics"},{"key":"key\n\t\t\t\t20171013034749_gks915-B10","doi-asserted-by":"crossref","first-page":"D146","DOI":"10.1093\/nar\/gkq1138","article-title":"lncRNAdb: a reference database for long noncoding RNAs","volume":"39","author":"Amaral","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013034749_gks915-B11","doi-asserted-by":"crossref","first-page":"D162","DOI":"10.1093\/nar\/gkl994","article-title":"Noncoding RNAs database (ncRNAdb)","volume":"35","author":"Szymanski","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013034749_gks915-B12","doi-asserted-by":"crossref","first-page":"D112","DOI":"10.1093\/nar\/gki041","article-title":"NONCODE: an integrated knowledge database of non-coding RNAs","volume":"33","author":"Liu","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013034749_gks915-B13","doi-asserted-by":"crossref","first-page":"D210","DOI":"10.1093\/nar\/gkr1175","article-title":"NONCODE v3.0: integrative annotation of long noncoding RNAs","volume":"40","author":"Bu","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013034749_gks915-B14","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkq1129","article-title":"Rfam: wikipedia, clans and the \u2018decimal\u2019 release","volume":"39","author":"Gardner","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013034749_gks915-B15","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/nature07672","article-title":"Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals","volume":"458","author":"Guttman","year":"2009","journal-title":"Nature"},{"key":"key\n\t\t\t\t20171013034749_gks915-B16","doi-asserted-by":"crossref","first-page":"3429","DOI":"10.1093\/nar\/gkg599","article-title":"Vienna RNA secondary structure server","volume":"31","author":"Hofacker","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013034749_gks915-B17","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/BF00818163","article-title":"Fast folding and comparison of RNA secondary structures","volume":"125","author":"Hofacker","year":"1994","journal-title":"Monatsh. Chem. Chem. Mon."},{"key":"key\n\t\t\t\t20171013034749_gks915-B18","doi-asserted-by":"crossref","first-page":"2911","DOI":"10.1093\/bioinformatics\/bth374","article-title":"Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences","volume":"20","author":"Bonnet","year":"2004","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013034749_gks915-B19","first-page":"358","article-title":"A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA","volume":"147","author":"Cesana","year":"2011","journal-title":"Gastroenterology"},{"key":"key\n\t\t\t\t20171013034749_gks915-B20","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1101\/gad.182121.111","article-title":"Suppression of progenitor differentiation requires the long noncoding RNA ANCR","volume":"26","author":"Kretz","year":"2012","journal-title":"Genes Dev."},{"key":"key\n\t\t\t\t20171013034749_gks915-B21","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1093\/bioinformatics\/btm595","article-title":"Prediction of both conserved and nonconserved microRNA targets in animals","volume":"24","author":"Wang","year":"2008","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013034749_gks915-B22","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkm391","article-title":"CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine","volume":"35","author":"Kong","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013034749_gks915-B23","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20171013034749_gks915-B24","doi-asserted-by":"crossref","first-page":"D290","DOI":"10.1093\/nar\/gkr1065","article-title":"The Pfam protein families database","volume":"40","author":"Punta","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013034749_gks915-B25","doi-asserted-by":"crossref","first-page":"3537","DOI":"10.1002\/pmic.200401303","article-title":"PRIDE: the proteomics identifications database","volume":"5","author":"Martens","year":"2005","journal-title":"Proteomics"},{"key":"key\n\t\t\t\t20171013034749_gks915-B26","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/nmeth725","article-title":"Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book","volume":"1","author":"Sadygov","year":"2004","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20171013034749_gks915-B27","doi-asserted-by":"crossref","first-page":"2105","DOI":"10.1002\/pmic.201000704","article-title":"Peptide identification quality control","volume":"11","author":"Vaudel","year":"2011","journal-title":"Proteomics"},{"key":"key\n\t\t\t\t20171013034749_gks915-B28","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1002\/pmic.201000595","article-title":"SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches","volume":"11","author":"Vaudel","year":"2011","journal-title":"Proteomics"},{"key":"key\n\t\t\t\t20171013034749_gks915-B29","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1093\/bioinformatics\/bth092","article-title":"TANDEM: matching proteins with tandem mass spectra","volume":"20","author":"Craig","year":"2004","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013034749_gks915-B30","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1038\/nbt1236","article-title":"Evaluation of DNA microarray results with quantitative gene expression platforms","volume":"24","author":"Canales","year":"2006","journal-title":"Nat. Biotechnol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/41\/D1\/D246\/18789333\/gks915.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T14:40:41Z","timestamp":1522680041000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/41\/D1\/D246\/1073870\/LNCipedia-a-database-for-annotated-human-lncRNA"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,10,5]]},"references-count":30,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2012,10,5]]},"published-print":{"date-parts":[[2013,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gks915","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2013,1,1]]},"published":{"date-parts":[[2012,10,5]]}}}